Re: [modeller_usage] modeling a chimeric protein

On 4/22/18 7:44 AM, Ayesha Fatima wrote:> is this the .ali file to give for alignment.

Yes, an alignment file like that should work fine.

> Which script should I use.

Since it's a chimera most conventional alignment scripts are not going to do the right thing for you, since they will try to make a global alignment of the two proteins, which is precisely not what you want. I would combine them manually, unless you have another structure of a linker region to which both will align.

Ben Webb, Modeller Caretaker